REPUBLIC OF

MINISTRY OF HEALTH (MOH)

PUBLIC HEALTHPUBLIC EMERGENCY HEALTH EMERGENCY OPERATIONS OPERATIONS CENTRE (PHEOC) CENTRE (PHEOC)

COVID-19 WEEKLY SITUATION REPORT

Issue NO: 33 Reporting Period: 12-18 October 2020 (week 42)

36,740 2,655 CUMULATIVE SAMPLES TESTED CUMULATIVE RECOVERIES 2,847 CUMULATIVE CONFIRMED CASES 55 9,152 CUMULATIVE DEATHS CUMULATIVE CONTACTS LISTED FOR FOLLOW UP

1. KEY HIGHLIGHTS  A cumulative total of 2,847 cases have been confirmed and 55 deaths have been recorded, with case fatality rate (CFR) of 1.9 percent including 196 imported cases as of 18 October 2020.  1 case is currently isolated in health facilities in the Country; and the National IDU has 99% percent bed occupancy available.  2,655 cases (0 new) have been discharged to date.  135 Health Care Workers have been infected since the beginning of the outbreak, with one death.  9,152cumulative contacts have been registered, of which 8,835 have completed the 14-day quarantine. Currently, 317 contacts are being followed, of these 92.1 percent (n=292) contacts were reached.  722 contacts have converted to cases to date; accounting for 25.3 percent of all confirmed cases.  Cumulatively 36,740 laboratory tests have been performed with 7.7 percent positivity rate.  There is cumulative total of 1,373 alerts of which 86.5 percent (n=1, 187) have been verified and sampled; Most alerts have come from Central Equatorial State (75.1 percent), Eastern Equatoria State (4.4 percent); State (3.2 percent) and the remaining 17.3 percent are from the other States and Administrative Areas.  As of 18 October, 24 Counties (30.0 percent) out of 80 Counties of the ten are affected (figure 4).

2. BACKGROUND South Sudan confirmed its first COVID-19 case on 5 April 2020. To date 2, 847 cases have been confirmed out of cumulative 36,740 tests performed by the National Public Health Laboratory (NPHL) and other decentralized Public Health Laboratories Networks in Nimule, Bor, and and UN clinics in , with 2,655 recoveries and 55 deaths, yielding the case fatality rate (CFR) of 1.9 percent. Up to 7.2 percent (n=205) confirmed cases were imported. South Sudan is classified as having clusters of transmission in general and community transmission in Juba, the capital city.

3. EPIDEMIOLOGY AND SURVEILLANCE Descriptive epidemiology

 This report includes analysis for 2,847 cases the Public Health Emergency Operation Centre (PHEOC) has line listed as confirmed cumulative cases. There are 2,655 recoveries and 55 deaths with case fatality rate (CFR) of 1.9 percent. Cases detected among South Sudanese nationals accounted for (79 percent) of all cases, whereas (12 percent) are foreigners, and 8 percent unknown. There have been 205 imported cases (9 new) registered to date coming mostly from Kenya (17), Uganda (32), Eretria (4), DRC (2), Somalia (1) and South Sudanese returnees (78), and unknowns (71).  Confirmed cases range from 2 months - 90 years of age with an average of 36.6 years. As for gender, 72.9percent of confirmed cases were diagnosed in men, 23.2% in women, and 3.9% unknown. Young men within the 30-39 age groups are the most at risk for COVID-19.  Only 21.0 percent (n=602) cases reported symptoms, of which the most frequent have been cough (404) , fever (351) , runny nose (257) , shortness of breath (230), fatigue (227) , headache (203) , sore throat (135), muscle aches (129), and others (226).

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REPUBLIC OF SOUTH SUDAN

MINISTRY OF HEALTH (MOH)  As of 18 October 2020, the affected Counties are alphabetically: Abyei (52), Aweil Center (8), Aweil East (5), Baliet (1), Ikotos (5), Juba (2,267), Maban (7), Magwi (3), Malakal (84), Nyirol (26), Rubkona (10), Rumbek North (1), Rumbek Center (22), Rumbek East (1), South Bor (32), Tonj North (1), Torit (40), Twic Warrap (3), Twic East (2),Uror (2),Wau (29), Yambio (7), Yei (23), Yirol West (1), Unknown (10).  New and cumulative, age, sex; frequency of symptoms; and geographical distribution of COVID-19 confirmed cases are shown in figures 1, 2, 3 and 4 and table 1 respectively.

Figure 1: New and cumulative confirmed COVID cases by notification date as of 18 October 2020

200 3,000

150 2,250

100 1,500

50 750

0 0

5-Jul

7-Jun

4-Oct

5-Apr

6-Sep

2-Aug 9-Aug

26-Jul 12-Jul 19-Jul

3-May

14-Jun 21-Jun 28-Jun

11-Oct 18-Oct

12-Apr 19-Apr 26-Apr

13-Sep 20-Sep 27-Sep

16-Aug 23-Aug 30-Aug

10-May 17-May 24-May 31-May

New cases 7-day moving average Cumulative cases

Figure 2. Frequency of symptoms among Figure 3. Age and sex distribution of § ‡ 0those reporting100 200 (n=602300 ) 400 500 COVID-19 confirmed cases (n=2 597 ) >70 yrs Cough 404 60-69 yrs Fever 351

50-59 yrs Runny Nose 257 40-49 yrs Shortness of… 230 30-39 yrs Fatigue 227 20-29 Age group yrs Headache 203 10-19 yrs Sore throat 135 Muscle aches 129 0-9 yrs Other 226 300 200 100 0 100 200 300 400 500 600 700 800 Female §Only 602 cases reported having symptoms. ‡2 597 cases have information regarding sex and age

Contact tracing summery

 As of 18 October 2020, the total number of contacts (old and new) that have been monitored has reached 9, 152. Out of these 96.5 percent (n=8,835) contacts have completed 14-day quarantine period.  Currently, 317 contacts are being followed of these 92.1 percent (n=292) contacts were reached.  722 contacts have converted to cases thus far; accounting for 25.3 percent of all confirmed cases.

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REPUBLIC OF SOUTH SUDAN

MINISTRY OF HEALTH (MOH)

Figure 4: Distribution of confirmed COVID-19 cases according to Counties Table 1: Summary of COVID-19 Cases by State as of 18 October 2020 Cases Deaths State New Cumulative New Cumulative Central Equatoria 5 2 291 0 40 Eastern Equatoria 0 47 0 2 Jonglei 0 62 0 1 Lakes 0 25 0 6 NBG 0 13 0 0 Unity 0 10 0 1 Upper Nile 0 92 0 4 Warrap (including Abyei) 0 56 0 0 WBG 0 29 0 0 Western Equatoria 0 7 0 0 Imported 0 205 0 1 Unknown 0 10 0 0 Pending classification 0 0 0 0 Total 5 2 847 0 55

4. PUBLIC HEALTH ACTION / RESPONSE INTERVENTIONS

4.1 COORDINATION AND LEADERSHIP  Coordination is ongoing in the Country through different architectures at National, States and County levels: National Task Force (NTF) providing high level strategic decisions; the National Steering Committee (NSC) providing both strategic and operational decisions/ guidance; the Technical Working Groups at both National and State levels; and the State Task Forces (STF), as well as County Committees (CC).  Ongoing COVID-19 Transitional Roadmap discussions by stakeholders including the NSC and the Inter-Agency Leadership Team for mainstreaming COVID-19 into other response and coordination structures aimed at strengthening incident management system in both the short and long terms for humanitarian and development activities.  The South Sudan Guidelines on COVID-19 was issued by Medical Advisory Panel (MAP) of the NTF. The Guides are currently under review by the NSC members and the TWGs, and will be updated accordingly.

4.2 LABORATORY  Cumulative 36,740 samples tested as of October 18, 2020.  Cumulative 2,847 positive cases confirmed across the country with 7.7% positivity rate.  South Sudan’s daily testing average positivity proportions this 1,000 2.00% reporting week is shown in figure 5. The trend line in gray 1.74% 1.76% 1.79% 1.80% shows the average percentage of tests that were positive 500 1.68% 2921.03 1.55%3810.52 4351.61 5181.93 5063.16 1.62%5131.75 1.60%4201.19 1.60% over the last 7 days. The orange bars show the percentage of 0 1.40% tests conducted each day that were positive.  The TWG has continued the implementation of the GeneXpert decentralization plan to cover Awiel, and later Daily Total Tests Yirol, Nzara, and Makpondu in Western Equatoria State Daily % Positive (WES).  Ongoing review of the recently issued MAP testing strategy Percentage positive tests (7-day moving average) and consensus to have wider discussion on the COVID-19 Algorithm and the use of RDT. Fig 5: Laboratory testing positivity data: 7-day count and moving average, 12-18 Oct 2020

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REPUBLIC OF SOUTH SUDAN

MINISTRY OF HEALTH (MOH)  All suspected EVD samples from Raja County tested negative for Ebola, Marburg, Rift Valley Fever (RVF), and yellow fever. The samples were also tested for an extra CCHF in the UVRI research center in Uganda; while further plan to test for arbovirus. 4.3 SURVEILLANCE  Epi-Surveillance and PoE TWGs provided specific language to modify the MAP recommendations document for two Protocols (1&2).  Multiple pillars are writing the roadmap to: a) improve generation and reporting of alerts at PoEs, POCs, refugee camps; b) improve overall community surveillance in the States and Administrative Areas; c) expand laboratory testing capacity at the mobile lab in Nimule; d) expand testing at the 10 GeneXpert sites; and e) integrate testing at the 7 of the 16 priority PoEs (excluding Juba International Airport).  TWG participated in the WHO-led RDT roundtable with Laboratory TWG and CDC to discuss uptake, deployment, and interpretation of results. Also discussed the operational aspects of RDT implementation, such as human resource, isolation/quarantine stations, and revisions to entry/exit requirements, training to improve lab and documentation /reporting systems.

 Data collection in the health workers’ retrospective survey ends on 18 October; preliminary report of findings will be shared.

4.4 CASE MANAGEMENT  The Minister of Health visited Wau COVID-19 facility and Medair Home Care Support System appreciated health care workers for the sacrifice demonstrated in the fight against COVID-19 by providing essential care. • Active patients by COB 12/10: 19  Currently there are 20 functional COVID-19 facilities in the Country, • Discharged: 11

and only one patient admitted in Juba. Total Enrolled Declined Admitted to IDU Deceased at Not Reached at time of first time of first qualified (Alerts + call call  17 facilities for referral systems were targeted, but to date 11 have confirmed cases) 24 70.8% 16.7% 0% 0% 12.5% been reached attributed to funding challenges for the procurement (17) (4) (0) (0) (3)

of ambulances. Total Male Female Asymptomatic Mild Moderate Severe Enrolled  Dr. John Garang IDU received 4 alerts in the past week, admitted 2 17 76.5% 23.5% 64.7% 35.3% 0% 0% (13) (4) (11) (6) (0) 0 suspects who turned negative and 1 positive case currently admitted and stable. 2 | South Sudan Public Health Emergency Operations center (PHEOC)  Alerts in Juba POC and Wau responded to and they were negative. Wau COVID 19 facility is functional.  Case Management services to IDPs and refugees on tack.  Mortality surveillance and dead body management standardization is on-going.  IMC Emergency Medical Team (EMT) composed of 1 ICU physician, 1 anesthesiologist, 1 ICU Nurse and 1 Biomedical Engineer commenced the assessment to have baseline for establishment of an ICU/HDU set up at Juba Teaching Hospital and JTH and Dr. John Garang IDU.

4.5 INFECTION PREVENTION AND CONTROL (IPC)  The Swiss Humanitarian Aid donated 440,000 masks to UNHCR, to boost the protection of frontline workers from COVID-19 targeting refugee hosting areas, filling critical PPE response gap especially in hard to reach areas where the majority of refugees are hosted.  Partners continue to scale up activities with improved collaboration of an integration of WASH services with RCCE, Health and Nutrition actors in health facilities, POCs, and communities at risk. Based on reports received from 12 partners, below are key countrywide achievements:  131 out of 600 people (22 percent) observed to use handwashing stations in public places (churches, health facilities, schools, markets, and other public places in Yar-got and Baac payams in (NBeG), Agoro payam in Magwi County (EES) and in Kor-Al-Amer and Jin-Quarter payams in (GUN).  6 out of 300 people ( 2 percent ) who received a face masks and actually wear them during sensitization activities organised by hygiene promoters in Rajaf (POCs) Payam in Juba County (CES) and in Kor-Al-Amer and Jin-Quarter payams in Maban County (GUN).  2, 297 people reached with critical WASH supplies/hygiene items and services in Baac and Madhol payams in Aweil East County (NBeG), Malual North and Malual West payams in Aweil North County ((NBeG) and Ayat West and Ayat East payams in Aweil West County (NBeG). 4

REPUBLIC OF SOUTH SUDAN

MINISTRY OF HEALTH (MOH)  20, 451 people engaged and reached with integrated COVID-19 and hygiene promotion services.  32,681 people reached with WASH facility upgrades through repairs, rehabilitation, and new construction in Renk Payam in (GUN), Malakal Payam in Malakal County (GUN), Anackdiar Payam in (GUN), in Rajaf (POCs) payam in Juba County (CES) in Wau Central and Wau North and Wau South Payams in Wau county (WBG)  8, 641 people were reached with cloth face masks distributed in communities in Malakal Payam in Malakal county (GUN State), in Juba and Rajaf Payams in Juba County (CES), in Wanyjok Payam in Aweil East County (NBeG), in Aroyo Payam in Aweil Centre County (NBeG), Malek Alel payam in Aweil South County (NBeG), Gokmachar payam in Aweil North County (NBeG) and in Malakal payam in Malakal County (GUN)  88 Health Workers and community WASH workers trained in IPC measures in Juba and Rajaf payams in Juba County (CES), Aroyo Payam in Aweil Centre County (NBeG) and Wanyjok Payam in Aweil East County (NBeG), Malek Alel payam in Aweil South County (NBeG) and Gokmachar payam in Aweil North County (NBeG)  15 health facilities including COVID-19 treatment facilities supported with PPE and IPC supplies in Renk Payam in Renk County (GUN state), in Juba and Rajaf Payams in Juba County (CES), in Wanyjok Payam in Aweil East County (NBeG), Aroyo Payam in Aweil Centre County (NBeG), Yambio Payam in Yambio County (WEQ), Malek Alel payam in Aweil South County (NBeG) and in Gokmachar payam in Aweil North County (NBeG)  2 triage and screening area set up as per SOP in Bunj Payam in Maban County (GUN) and in Aroyo payam in Aweil Centre County (NBeG)  205 hand washing stations installed in health facilities and communities and provided with soap or 0.05% chlorine solution.

4.6 RISK COMMUNICATION AND COMMUNITY ENGAGENT (RCCE)- NSTR

4.7 LOGISTICS AND OPERATION SUPPORT (LOS)  Following the arrival of SSHF funded COVID-19 PPE commodities in South Sudan, WFP through the Logistics Cluster, and WHO, as co- leads of the Operational Support and Logistics Pillar of the National Response Plan, re-launched the Personal Protective Equipment (PPE) Common Request System, aiming at consolidating requests of in-country COVID-19 PPE commodities. During the reporting week, 33 request forms received from 17 organisations. All request forms have been approved by the Inter-Agency technical team on 14 October, totalizing 1,455,719 PPE allocated from the common pool to be received in 205 locations across South Sudan.  From 12 to 16 October, a total of 21 COVID-19 samples have been transported from four locations across South Sudan (Agok, Aweil, Rubkona and Rumbek) to Juba for testing.  The movement of Rapid Response Team for COVID-19 related activities continues to be supported by the provision of 10 vehicles both in Juba and Nimule.

4.8 POINTS OF ENTRY (POE)  13,793 travelers underwent primary screening at various IOM Health promoter in Wunthou PoE -Renk screening point enlightening screening points in Juba, Wau, Nimule, and Maban-(5,517-JIA, travelers on hand washing and distancing. (Photo credit by Lam Deng) 3,327-Nimule, 2,007-Wau, 73-Wunthuo-Renk, and 368-Amiet- Abyei conducted by the IOM; and 2,501 screening conducted in Nadapal by Comitato Collaborazione Medico (CCM). Four travelers were referred to secondary screening in Nadapal (2) and Nimule (2).  HDC/ UNHCR partner conducted screening in refugees camp in Maban (Shatta, Khortumbark, Dangaji and Kaya) for a total of 15,388 refugees, of which 229 were referred for secondary screening and 12 alerts raised. 5

REPUBLIC OF SOUTH SUDAN

MINISTRY OF HEALTH (MOH)  The POE TWG is currently updating the Standard Operating Procedures (SOPs) for border crossings and camp and camp like settings based on the updated Case Definition for South Sudan.  CORE Group is planning to conduct training for the newly formed Cross Border committee in Nimule in the coming week.

5. MAJOR CHALLENGES

 Challenges in reaching patients for home-based care due to incorrect phone numbers.  Testing from the states where no testing facility is available, still problematic, (sample collection not done in a timely manner as well as transportation to Juba, compounded by poor motivation due to unpaid incentives for RRT.  Contacts refusing to comply with quarantine measures or denying exposure with the case though they are known to be a contact.  Funding challenges across pillars especially for case management and PoE.  Limited PPE availability for COVID-19 facilities and Triage points highlighted across all States. In Unity State, lack of PoE screening, IPC supplies, and ambulance was raised. While EES, two Medical Officers resigned from Torit State COVID-19 Case Management team due to lack of risk allowances.  Despite the high level of knowledge registered, there still persistent low perception of risk among the population requiring regular advocacy by all stakeholders including NSC. Stigma reported against COVID-19 patients also discouraging new cases to seek for medical care.  Documentation of surveillance, contact tracing, and RRT trainings conducted by partners in the States and Counties lack consistent reporting to PHEOC, hence requires follow-up by State health clusters and emphasis by MoH/PHEOC.  Limited access and mobility to communities and health facilities due to heaving rains/ flooding, poor logistics, and insecurity. Also Protest by Youths in Upper Nile (Renk and Melut) interrupted some COVID-19 intervention including case management.

6. RECOMMENDATIONS AND PRIORITY FOLLOW UP ACTIONS

 Review and update of South Sudan COVID-19 Guidelines on COVID-19, and dissemination to wider audience.  Revise and update the strategies for surveillance, testing, case management and contact tracing as the outbreak evolves.  NSC take up the issue of distribution of VTMs and kits to the States and implementing partners so that they can actually implement the lab testing strategy and improve COVID-19 surveillance and testing rates across the Country.  Establishment of remote meeting devices to the operational COVID-19 facilities for online experience sharing and trainings.  Continue engagement with the Juba City Council and State authorities for mitigation campaign aimed at reducing the risk of COVID-19 transmission during community events including funerals and wedding.  Scale up risk communication and community engagement to address the stigma associated with COVID-19 in South Sudan especially with target groups of IDPs living in PoC camps and with community contacts observing quarantine in large households.

7. CONCLUSIONS

Ongoing coordination and collaboration amongst actors including National Task Force (NTF), National Steering Committee (NSC), State Tasks Forces (STFs), MOH/PHEOC and other government Ministries, agencies and departments is needed to strengthen the COVID-19 outbreak preparedness and response mechanisms. Furthermore, update and disseminate the South Sudan Guidelines for COVID-19 to wider audience.

For any clarifications, please contact Name Title Contact Email address 1 Dr. Richard Lako COVID -19 Incident Manager-MOH +211926592520 [email protected] 2 Mathew Tut PHEOC Manager +211916010382 [email protected] 3 Henry Gray COVID -19 Incident Manager-WHO 211928740879 [email protected] 4 Stella Ajwang HAO, OCHA COVID-19 Secretariat +211922473132 [email protected]

FOR MORE INFORMATION and NOTIFICATION: Call: 6666 (TOLL FREE LINE) or +211922202028; Email: [email protected]

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